Preprocessing and Traditional fMRI Analysis Tools
- SPM (Statistical Parametric Mapping): http://www.fil.ion.ucl.ac.uk/spm/
- FSL (FMRIB Software Library): https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
- ANTs (Advanced Normalization Tools): http://stnava.github.io/ANTs/
- Freesurfer: https://surfer.nmr.mgh.harvard.edu/
- AFNI (Analysis of Functional Neuroimages): https://afni.nimh.nih.gov/
- BWT (Brain Wavelet Toolbox): http://www.brainwavelet.org/
Resting-State fMRI Analysis Tools
- CONN functional connectivity toolbox: https://www.nitrc.org/projects/conn/
- C-PAC (Configurable Pipeline for the Analysis of Connectomes): https://fcp-indi.github.io/
- DPARSF (Data Processing Assistant for Resting-State fMRI): http://rfmri.org/DPARSF
- REST resting-state fMRI data analysis toolkit: http://restfmri.net/forum/index.php
Other Analysis Tools
- PRoNTo (Pattern Recognition for Neuroimaging Toolbox): http://www.mlnl.cs.ucl.ac.uk/pronto/
- BCT (Brain Connectivity Toolbox): https://sites.google.com/site/bctnet/
- DKE (Diffusional Kurtosis Estimator) software: http://academicdepartments.musc.edu/cbi/dki/
- MENGA (Multimodal Environment for Neuroimaging and Genomic Analysis): https://www.nitrc.org/projects/menga/
- ASL (Arterial Spin Labeling) Data Processing Toolbox: https://cfn.upenn.edu/~zewang/ASLtbx.php